Genome Structure and Phylogenetic Analysis of Lettuce Infectious Yellows Virus, a Whitefly-Transmitted, Bipartite Closterovirus

Abstract

We report the complete nucleotide sequences of lettuce infectious yellows virus (LIYV) RNAs 1 and 2. LIYV RNA 1 is 8118 nucleotides and includes three open reading frames (ORFs). Computer-assisted analysis of LIYV RNA 1 ORFs identified domains for a papain-like protease, methyltransferase (MTR), RNA helicase (HEL), and RNA-dependent RNA polymerase (RdRp). We suggest that the RdRp domain is expressed independently of the other replication-associated domains via a + 1 ribosomal frameshift. Amino acid sequences of the MTR, HEL, and RdRp show highly significant similarity to the homologous sequences from other closteroviruses and lower similarity to the respective proteins of tobamoviruses, tobraviruses, hordeiviruses, bromoviruses, and furoviruses. LIYV RNA 2 is 7193 nucleotides and includes six ORFs. These ORFs include a gene array that is characteristic of the closteroviruses: ORFs encoding a small membrane protein, a homologue of the HSP70 family of chaperone proteins, a protein whose function is unknown, the coat protein, and a diverged duplicate of the coat protein. LIYV is distinguished from the monopartite closteroviruses in the following ways: its genome consists of two RNAs, the positions of the coat protein gene and its diverged duplicate are reversed, and LIYV includes ORFs that are unrelated to ORFs found in other closteroviruses.

Complete genome structure and phylogenetic analysis of little cherry virus, a mealybug-transmissible closterovirus.

“…A. Agranovsky W. Jelkmann, B. Fechtner and A. A. Agranovsky closterovirus genomes have revealed no statistically significant similarity among them, apart from the C-terminal PCP domain (Karasev et al, 1995 ;Klaassen et al, 1995). Our analysis also failed to identify any related sequences in the LChV and BYV proteins upstream of their PCP (Fig.…”

“…3) showed branching of BYV, BYSV, CTV and LIYV compatible with that in the previous POL reconstructions (cf. Dolja et al, 1994 ;Klaassen et al, 1995). Further, our analysis suggested that the aphid-transmissible BYV, BYSV and CTV, on the one hand, and the whiteflytransmissible LIYV, SPSVV and cucumber chlorotic spot virus (CCSV) and the mealybug-transmissible LChV, on the other, represent two distinct evolutionary lineages (Fig.…”

“…Related PCP domains have been predicted in the ORF 1a products of CTV (Karasev et al, 1995), LIYV (Klaassen et al, 1995) and some other closteroviruses (reviewed in Agranovsky, 1996). Comparisons of the LChV ORF 1a product with those of BYV, LIYV and SPSVV allow prediction of a similar PCP domain with a cleavage site between Gly-619 and Ser-620 (Figs 1 b-d and 2).…”

“…As the anchor ligation method (Keim-Konrad & Jelkmann, 1996) failed to yield PCR products, tailing of the dsRNA with rATP followed by applying a 5h\3h RACE protocol (Boehringer Mannheim) was used. The 5h-terminal residue determined from the minus strand of LChV dsRNA is a C. Genomic RNAs of other closteroviruses start with an A or G (Agranovsky et al, 1994 ;Klaassen et al, 1995 ;Karasev et al, 1995), as is characteristic for the residues next to the 5h-m7G cap in eukaryotic messengers. However, Karasev et al (1995) Local similarity searches were performed using the program ALIGN-2 from the GENEBEE package (Brodsky et al, 1990).…”

“…Starting four nucleotides after the UAA stop codon of ORF 1b is ORF2 (nt 8503-8602), which codes for a small hydrophobic protein of 36 aa (4 kDa) containing the N-terminal stretch of non-polar amino acids (data not shown) predicted to form a transmembrane helix in the equivalent proteins of BYV, beet yellow stunt virus (BYSV), CTV and LIYV (Klaassen et al, 1995). ORF 2 overlaps the first 11 nucleotides of ORF 3, which encodes a 70 kDa HSP70 homologue.…”